scholarly journals The Proton in Biochemistry: Impacts on Bioenergetics, Biophysical Chemistry, and Bioorganic Chemistry

2021 ◽  
Vol 8 ◽  
Author(s):  
Todd P. Silverstein
Keyword(s):  
Atp Hydrolysis ◽  
Hydration Shell ◽  
High Mobility ◽  
Bulk Water ◽  
Ph Effects ◽  
Atomic Particle ◽  
Waste Products ◽  
Hydrated Proton ◽  
Key Aspects ◽  
Acid Waste

The proton is the smallest atomic particle, and in aqueous solution it is the smallest hydrated ion, having only two waters in its first hydration shell. In this article we survey key aspects of the proton in chemistry and biochemistry, starting with the definitions of pH and pKa and their application inside biological cells. This includes an exploration of pH in nanoscale spaces, distinguishing between bulk and interfacial phases. We survey the Eigen and Zundel models of the structure of the hydrated proton, and how these can be used to explain: a) the behavior of protons at the water-hydrophobic interface, and b) the extraordinarily high mobility of protons in bulk water via Grotthuss hopping, and inside proteins via proton wires. Lastly, we survey key aspects of the effect of proton concentration and proton transfer on biochemical reactions including ligand binding and enzyme catalysis, as well as pH effects on biochemical thermodynamics, including the Chemiosmotic Theory. We find, for example, that the spontaneity of ATP hydrolysis at pH ≥ 7 is not due to any inherent property of ATP (or ADP or phosphate), but rather to the low concentration of H+. Additionally, we show that acidification due to fermentation does not derive from the organic acid waste products, but rather from the proton produced by ATP hydrolysis.

Anaerobic Storage of Activated Sludge: Effects on Conditioning and Dewatering Performance

1993 ◽  
Vol 28 (1) ◽  
pp. 109-116 ◽  
Author(s):  
Jacob H. Bruus ◽  
Jimmy R. Christensen ◽  
Hanne Rasmussen
Keyword(s):  
Organic Matter ◽  
Activated Sludge ◽  
Wastewater Treatment Plants ◽  
Treatment Plant ◽  
Working Hours ◽  
Bulk Water ◽  
Optimal Dosage ◽  
Nitrogen And Phosphorus ◽  
Waste Products ◽  
Anaerobic Storage

Since dewatering equipment is commonly operated only during normal working hours, activated sludge must often be stored in an anaerobic condition prior to conditioning. It is the objective of this study to investigate the influence of anaerobic storage on conditioning requirements and dewatering performance on a laboratory scale. Sludges were collected at two large treatment plants (removal of organic matter, nitrogen and phosphorus) and one small treatment plant (removal of organic matter). Thickened activated sludges from the three wastewater treatment plants were stored anaerobically in the laboratory and analyzed frequently during fourteen days of storage. Both organic and inorganic conditioning was used. Turbidity and Dissolved Organic Carbon (DOC) in the sludge bulk water increased as a result of the anaerobic storage. These parameters indicated a release of colloids, dissolved exopolymers and fermentation waste products such as fatty acids to the bulk water. These constituents consumed additional cationic polyelectrolyte. Filterability at the optimal dosage of polyelectrolyte was not affected by anaerobic storage. Therefore, polyelectrolyte requirements are governed by the bulk water constituents, whereas filterability of the sludge is determined by the degree of sludge floc conditioning. Iron requirements seemed unaffected by anaerobic storage, but lime requirements to obtain good filterability increased with anaerobic storage time.

scholarly journals Protein conformational entropy is not slaved to water

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Bryan S. Marques ◽  
Matthew A. Stetz ◽  
Christine Jorge ◽  
Kathleen G. Valentine ◽  
A. Joshua Wand ◽  
...  
Keyword(s):  
Protein Function ◽  
Hydration Shell ◽  
Nmr Relaxation ◽  
Bulk Water ◽  
Side Chain ◽  
Conformational Entropy ◽  
Solvent Water ◽  
Protein Molecules ◽  
Protein Functions ◽  
Internal Side

Abstract Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The “solvent slaving” model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side chain dynamics of several proteins are unaffected by changes to the hydration layer and bulk water. These observations indicate that the participation of conformational entropy in protein function is not dictated by the interaction of protein molecules and solvent water under the range of conditions normally encountered.

The Structural and Dynamic Properties of some Transition Metal Aqua Cations: Results from Neutron Scattering

1995 ◽  
Vol 50 (2-3) ◽  
pp. 247-256 ◽  
Author(s):  
G. W. Neilson ◽  
S. Ansell ◽  
J. Wilson
Keyword(s):  
Transition Metal ◽  
Neutron Scattering ◽  
Dynamic Properties ◽  
Hydration Shell ◽  
Electrolyte Solutions ◽  
Bulk Water ◽  
Water Molecules ◽  
Quasielastic Neutron ◽  
Quasielastic Neutron Scattering ◽  
Insight Into

Abstract The following paper comprises a survey of the role neutron scattering methods have played to help understand the origins of the diverse properties of electrolyte solutions which contain transition metal cations. It is seen how neutron diffraction and isotopic substitution is able to resolve the local structure around contrasting ions, such as Cr3+ , Ni2+, Fe3+ , Fe2+, Cu2+, without recourse to sophisticated modelling procedures. Quasielastic neutron scattering (QNS) provides insight into the dynamics of the protons in solution. The results enable one to distinguish between cations whose water molecules are coordinated on time scales larger than 5 x 10-9 s, shorter than 10-10s, or intermediate between those two limits. QNS also provides information on the existence of a second relatively short-lived hydration shell distinct from the bulk water.

The dipole moment of water in the first hydration shell of a monovalent ion

1968 ◽  
Vol 46 (21) ◽  
pp. 2407-2411 ◽  
Author(s):  
Dieter K. Ross
Keyword(s):  
Dielectric Constant ◽  
Dipole Moment ◽  
Continuous Medium ◽  
Hydration Shell ◽  
Bulk Water ◽  
Water Molecules ◽  
The Mean ◽  
Monovalent Ion ◽  
Coordinated Water ◽  
First Hydration Shell

The mean dipole moment of the water molecules in contact with a monovalent ion is estimated. The first hydration shell of a spherical ion is assumed to contain either four or six coordinated water molecules, while the water molecules outside this shell are replaced by a continuous medium whose dielectric constant is that corresponding to bulk water at 25 °C. It is found that the dipole moment induced in the attached water molecules is comparable with its permanent dipole moment.

scholarly journals Tracking oxidation-induced alterations in fibrin clot formation by NMR-based methods

2021 ◽  
Author(s):  
Wai Hoe Lau ◽  
Nathan J. White ◽  
Tsin Wen Yeo ◽  
Russell L. Gruen ◽  
Konstantin Pervushin
Keyword(s):  
Translational Motion ◽  
Hydration Shell ◽  
Coagulation Factor ◽  
2D Nmr ◽  
Fibrin Clot ◽  
Bulk Water ◽  
Surface Relaxation ◽  
Methionine Oxidation ◽  
Fibrin Polymerization ◽  
Fibrin Gels

Abstract Plasma fibrinogen is an important coagulation factor that is susceptible to post-translational modification by oxidants. We have reported altered fibrin polymerization and increased methionine oxidation in fibrinogen after exposure to hypochlorous acid (HOCl), and similarly in the fibrinogen of severely injured trauma patients. Molecular dynamics suggests that methionine oxidation offers a mechanistic link between oxidative stress and coagulation through fibrin protofibril lateral aggregation by disruption of AαC domain structures. However, experimental evidence explaining how HOCl oxidation impairs fibrinogen structure and function has not been demonstrated. We used polymerization studies and two dimensional-nuclear magnetic resonance spectrometry (2D-NMR) to test the hypothesis that HOCl oxidation alters fibrinogen conformation in the prefibrillar state and T2 water surface relaxation of fibrin fiber assemblies. We found that both HOCl oxidation of purified fibrinogen and addition of HOCl-oxidized fibrinogen to plasma disrupted fibrin polymerization similarly to competitive inhibition of polymerization using a recombinant AαC fragment (AαC 419–502). DOSY NMR measurement of 1H fibrinogen at 25oC demonstrated that fibrinogen oxidation increased translational diffusion coefficient by 17.4%, suggesting a more compact and rapidly translational motion of the protein with oxidation. 2D-NMR analysis of control plasma fibrin gels indicated that water existed in two states, namely intermediate (T2i) in the hydration shell of fibrin fibers, and bulk (T2) within the gel. T2 relaxation of bulk water protons was decreased 2-fold in oxidized fibrin gels and was inversely proportional to gel fiber density (T2). The fast exchange of water protons between hydration shell (T2i) and bulk water, indicating oxidation increased fiber hydration and formed densely packed fibrin gels. We have confirmed experimentally that HOCl oxidation affected native fibrinogen and fibrin gel structures and have demonstrated that NMR can serve as a valuable tool to probe the oxidative rearrangement of fibrin clot structure.

scholarly journals Protein-Water and Water-Water Long-Time Relaxations in Protein Hydration Water upon Cooling—A Close Look through Density Correlation Functions

Molecules ◽  
2020 ◽  
Vol 25 (19) ◽  
pp. 4570
Author(s):  
Lorenzo Tenuzzo ◽  
Gaia Camisasca ◽  
Paola Gallo
Keyword(s):  
High Temperatures ◽  
Time Scale ◽  
Hydration Shell ◽  
Bulk Water ◽  
Hydration Water ◽  
Density Correlation ◽  
Nearest Neighbours ◽  
Long Time ◽  
Dynamics Simulations ◽  
Protein Fluctuations

We report results on the translational dynamics of the hydration water of the lysozyme protein upon cooling obtained by means of molecular dynamics simulations. The self van Hove functions and the mean square displacements of hydration water show two different temperature activated relaxation mechanisms, determining two dynamic regimes where transient trapping of the molecules is followed by hopping phenomena to allow to the structural relaxations. The two caging and hopping regimes are different in their nature. The low-temperature hopping regime has a time scale of tenths of nanoseconds and a length scale on the order of 2–3 water shells. This is connected to the nearest-neighbours cage effect and restricted to the supercooling, it is absent at high temperature and it is the mechanism to escape from the cage also present in bulk water. The second hopping regime is active at high temperatures, on the nanoseconds time scale and over distances of nanometers. This regime is connected to water displacements driven by the protein motion and it is observed very clearly at high temperatures and for temperatures higher than the protein dynamical transition. Below this temperature, the suppression of protein fluctuations largely increases the time-scale of the protein-related hopping phenomena at least over 100 ns. These protein-related hopping phenomena permit the detection of translational motions of hydration water molecules longly persistent in the hydration shell of the protein.

scholarly journals The Physiological Action of Abnormally High Temperatures on Poikilotherm Animals

1940 ◽  
Vol 17 (4) ◽  
pp. 386-395
Author(s):  
G. S. FRAENKEL ◽  
G. V. B. HERFORD
Keyword(s):  
Oxygen Consumption ◽  
High Temperature ◽  
Partial Pressure ◽  
High Temperatures ◽  
Oxygen Pressure ◽  
Partial Pressure Of Oxygen ◽  
Waste Products ◽  
Physiological Action ◽  
Very High ◽  
Acid Waste

The oxygen consumption of blowfly larvae at sublethal and lethal high temperatures at the beginning of the determination is entirely dependent on the oxygen pressure, but after about 1 hr. at 42°C. it is higher at 20 and 10% partial pressure of oxygen than at either 100 or 5%. Death at high temperatures is not due to lack of oxygen, but may be due to the accumulation of acid waste products of the metabolism. The basal oxygen consumption remains unchanged for some time after the organism has been irreversibly injured by the high temperature. Blowfly larvae resist the damaging effect of high temperatures slightly better in air (20% oxygen) than in either very high (100%) or very low (less than 10%) concentrations of oxygen.

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